Universal method for extracting nucleic acid molecules from a diverse population of one or more types of microbes in a sample

Abstract

Disclosed herein are methods of extracting genetic material from a diverse population of one or more types of microbes in a sample. Microbes can be prokaryotes or eukaryotes and may include bacteria, archaea, fungi, protozoa, helminths, parasites, viruses, phages, and others. Extraction may be from a single sample and subsequent identification may be through a molecular method such as qPCR, PCR, RFLP, SSCP, allele specific PCR, targeted sequencing, pull down sequencing, whole shotgun sequencing, or other methods. Also provided are methods that include extracting nucleic acid molecules from a variety of organisms such as fungi (i.e., Saccharomyces spp.), animal cells ( Bos taurus ), plants (e.g., Hordeum vulgare ) from the gut of a human subject, performing a metagenomics analysis therefrom, and determining a probiotic treatment or dietary guidance for the subject based on the metagenomics analysis.

1 - 73 . (canceled) 
     
     
         74 . A method of detecting, diagnosing and/or treating a subject comprising administering to the subject a formulation comprising a probiotic, pre-biotic, metabolite of the gut microbiome, or combination thereof, thereby causing a reduction or elimination of an opportunistic pathogen or a disease or disorder causing microbe of the gut. 
     
     
         75 . The method of  claim 74 , further comprising detecting the opportunistic pathogen or the disease or disorder causing microbe of the gut. 
     
     
         76 . The method of  claim 75 , further comprising isolating the opportunistic pathogen or the disease or disorder causing microbe of the gut. 
     
     
         77 . The method of  claim 75 , wherein the opportunistic pathogen or the disease or disorder causing microbe of the gut is from a sample of the subject. 
     
     
         78 . The method of  claim 74 , further comprising administering an isolated microbe from a sample obtained from the subject to the subject to reduce or eliminate the opportunistic pathogen or the disease or disorder causing microbe of the gut. 
     
     
         79 . The method of  claim 74 , wherein the probiotic comprises a microbe isolated from a sample obtained from the subject. 
     
     
         80 . The method of  claim 74 , further comprising diagnosing the disease or disorder in the subject by detecting a microbe of the gut obtained from the subject. 
     
     
         81 . The method of  claim 80 , wherein the disease or disorder is selected from autism spectrum disorder, mood disorder, chronic fatigue, infection, necrosis, inflammation, autoimmune, hemorrhage, weight loss, metabolic disorder, irritable bowel disorder, diabetes 1 or 2, rheumatoid arthritis, cancer, and cardiovascular disorder. 
     
     
         82 . The method of  claim 81 , wherein the disease or disorder is autism spectrum disorder. 
     
     
         83 . The method of  claim 74 , wherein the disease or disorder is selected from those set forth in Tables 5 or 6. 
     
     
         84 . The method of  claim 80 , further comprising administering a microbe to the subject to treat the disease or disorder, wherein the microbe is optionally isolated from a sample obtained from the subject. 
     
     
         85 . The method of  claim 84 , wherein the disease or disorder is autism spectrum disorder. 
     
     
         86 . The method of  claim 74 , wherein the probiotic comprises one or more microbes selected from those set forth in Tables 5-15. 
     
     
         87 . The method of  claim 86 , wherein the one or more microbes is isolated from a gut sample obtained from the subject. 
     
     
         88 . The method of  claim 87 , wherein the one or more microbes is selected from the group consisting of  Clostridium bolteae, Bifidobacterium lactis, Lactobacillus acidophilus, Bifidobacterium longum, Bifidobacterium bifidum, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus gasseri, Lactobacillus salivarius, Lactobacillus rhamnosus, Lactobacillus bulgaricus, Bacillus coagulans , and any combination thereof. 
     
     
         89 . The method of  claim 74 , wherein presence of a  Blastocystis  genus organisms is reduced in the subject. 
     
     
         90 . The method of  claim 89 , wherein the  Blastocystis  genus organism is  B. hominis.    
     
     
         91 . The method of  claim 74 , wherein presence of  Clostridium bolteae, Toxoplasma gondii, Klebsiella pneumonia, Candidatus Methanomassillicoccus intestinalis  or  C. difficile  is reduced in the subject. 
     
     
         92 . The method of  claim 87 , wherein the one or more microbes is selected from the group consisting of  Bacillus coagulans, Bacillus indicus, Bacillus lichenformis, Bacillus subtilis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium coagilans, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Bifidobacterium subtilis, Enterococcus faecium, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus delbrueckii, Lactobacillus gasseri, Lactobacillus helveticus, Lactobacillus lactis, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactobacillus salivarius, Saccharomyces boulardii, Streptococcus thermophiles, Lactobacillus buchneri, Lactobacillus fermentum, Lactobacillus crispatus, Bifidobacterium catenulatum, Bifidobacterium pseudocatenulatum , and combinations thereof. 
     
     
         93 . The method of  claim 84 , wherein longevity and/or aging of the subject is improved. 
     
     
         94 . The method of  claim 74 , further comprising confirming a shift and/or predicting a shift or a change in microflora of the subject using short, branched, or chemical fatty acid analysis of the subject. 
     
     
         95 . The method of  claim 94 , wherein the fatty acid analysis includes detecting a marker selected from butyrate, propionate, acetate, or other fatty acid. 
     
     
         96 . The method of  claim 94 , wherein the fatty acid analysis is used to determine differences between diagnosed autism spectrum disorder and normal phenotype. 
     
     
         97 . A method of treating autism spectrum disorder in a subject comprising administering to the subject a probiotic including one or more microbes as set forth in Table 15 causing a reduction of  Clostridium bolteae  in the subject, thereby treating autism spectrum disorder in the subject. 
     
     
         98 . The method of  claim 97 , wherein the one or more microbes is selected from the group consisting of  Bifidobacterium lactis, Lactobacillus acidophilus, Bifidobacterium longum, Bifidobacterium bifidum, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus gasseri, Lactobacillus salivarius, Lactobacillus rhamnosus, Lactobacillus bulgaricus , and  Bacillus coagulans.